Problem making index

[CormacKinsella]

Hi there, I'm on MacOS, I used makeDB.sh to download the progenomes and viral protein set, but after this I get the following error message: (command used was: makeDB.sh -p -v -t 1)

Extracting file taxdump.tar.gz Creating directory genomes/ Extracting protein sequences from downloaded files... xargs: illegal option -- i usage: xargs [-0opt] [-E eofstr] [-I replstr [-R replacements]] [-J replstr] [-L number] [-n number [-x]] [-P maxprocs] [-s size] [utility [argument ...]]

What am I doing wrong?

Thanks in advance!

[pmenzel]

Hi, that is a problem in makeDB.sh when running it on MacOS. Will try to fix it quickly! Peter

[charlesreid1]

I'm on the case...

[charlesreid1]

Hi @pmenzel, your proposed fix worked. Changing the xargs commands in lines 238 and 256 to

xargs -n 1 -P $parallelConversions -IXX gbk2faa.pl XX XX.faa

ran through the whole makeDB process smoothly on my Mac.

[charlesreid1]

Also, just for informational purposes, if you find it bewildering the way that Mac command line utilities only share 90% of the command line flags as their Linux counterparts (xargs, grep, ls, sed, etc), it's because Mac is using the BSD version of all those utilities (b/c underlying Darwin), while Linux uses the GNU version. A quick check online for the man page for the BSD versions should do it.

[pmenzel]

Thanks @charlesreid1 for testing and the PR!

@CormacKinsella Please get the latest version from github via

git clone https://github.com/bioinformatics-centre/kaiju.git

and then compile it with

cd kaiju/src
make

Afterwards, try running kaiju/bin/makeDB.sh -p -v again.

[CormacKinsella]

many thanks both!

[pmenzel]

Fix is now included in version 1.6.2.